How to justify the proteins by their pathways in the discussion for research paper?

Question

[arjahejo]

Kindly guide me, how can i justify the keg pathways of proteins in the discussion for research paper ?

[ATpoint]

Look, why don't you spend 20min of quality time to post what exactly your task is, what you have done so far and what you are struggling with right know. The way you have been posting things here so far 1) does not allow to understand what you are actually doing & 2) does not motivate people to help, so aim for some clear language.

[GenoMax]

You have not done a good job of providing complete information in your past threads (e.g. Anyone please guide me, i am trying it since last 5 months. ) nor are you laying out a detailed report of what you have done so far. If you are not able to formulate a logical explanation looking at the results (which we can't see) how can we give you an answer for this question? You should look at similar papers to see how those authors tackled this problem.

Answer 1

[Kevin Blighe]

That is a difficult question to answer.

Some journals (the very top journals) just won't accept any inferences/conclusions that you make from in silico pathway analyses alone. You will require validation results performed in the wet-lab to back up the findings. Other journals will fully accept such conclusions. The benefit of using KEGG, however, is that it already has a good World reputation and is curated, which means, at least from what I understand, that the pathways in KEGG are screened by human eyes and have experimental backing.

The way that people bring in things like KEGG into their writing is through the use of the conditional tense (could, would, ought to, etc.), and through statements like "these findings will require further validation". However, using statements like this, you're already implying that you're targeting a journal of impact factor <10.

Enrichment analysis on pathways also allows you to derive P values that provide more evidence that a particular pathway will be disturbed in your condition of interest. If a KEGG pathway contains 20 genes, all of which are down-regulated in your study, then it's a good sign that this particular pathway will be affected, and the enrichment P value would be virtually nil / zero.

Just my own 2 cents!

[GenoMax]

While you meant well OP is not actually looking to publish (far as we know). This is some sort of an exercise that his mentor has assigned (without any follow-up help, inferred conclusion). Apparently he has been working on this past for 5+ months without a cohesive conclusion as yet.

[Kevin Blighe]

Ah! - I see. I've only been here for 4 weeks. Interesting place...